Naruto: Pitch-Black DNA
by Kento-hish17
Summary: On the night of the Scroll Incident, a knowing Naruto secretly tricks Mizuki into showing his true colors. After learning the Kage Bunshin to humor the man, he finds two seals and releases them, becoming a pair of creatures during the confrontation. Afterwards, he enters his mind to meet Darkrai and Deoxys, finding he now had three new Kekkei Genkai.


A/N: _Pokemon! Pokemon! Pokemon! _Let's do it! :D Hey guys, we got NarutoxPokemon now! This will feature _technically _only two pokemon, but it will have a cool twist. I'm sure a lot of you know about Deoxys fusions, and I've seen a couple of awesome Darkrai fusions. Someone(s) has/have created multiple fusions of Deoxys, some invasion of the pokemon collecting DNA of everyone, and one person on Youtube (SuperSonicGX) has done twenty videos of fusing Darkrai with several pokemon, creating some awesome combos. It was pretty cool and I haven't read any good fanfics of Naruto with Deoxys. So, here's my try.

EDIT: I thank guest Z.L.C. for correcting my use of the word teleKINESIS instead of telePATHY.

Disclaimer: I don't own Naruto or Pokemon

"Hey"- Human speech

'_Hey'_- Human thought

"**Hey"**- Jutsu/Attack/Demon speech

'_**Hey'**_- Demon thought

Let's begin

Naruto was jumping through the trees, carrying the Forbidden Scroll of Seals on his back, his face a wall of concentration. _'Mizuki-teme must think I'm a real idiot. There's no way this is an auxiliary test for the genin exam, especially if it's something like stealing the Forbidden Scroll. Ojii-san told me time and again that, in the wrong hands, this scroll was incredibly dangerous. Thank Kami he let me take the scroll to weed out the traitor.' _Naruto thought as he scowled at the memories of Iruka-sensei failing him. He knew the man was truly sorry for it, and that the same silver-haired Chuunin was the reason for his failure; he felt foreign chakra enter his system and disrupt his control, resulting in the singular pathetic excuse of a clone attempt. Mizuki planned all of this.

Deciding to humor the traitor, Naruto set down near the agreed-upon shed and laid the scroll down. Ojii-san said he could look in the scroll, but not attempt any of the techniques; classic excuse of 'look but don't touch.'

As if he was going to listen. He knew about everything. The fox, his parents, Sarutobi hiding their identities from him for his safety from enemies of his parents within and outside the village, even his godparents, the Sannin Jiraiya and Tsunade. The former never checked in on him, opting to 'work on his spy network.' (Read: research for his perverted books) And Tsunade was wallowing in self-pity about her dead lover and brother, blaming the village for her misfortune, and spending away the Senju fortune with gambling, which she sucked at, and alcohol.

How'd he now all this? The very first thing he listed, the fox.

**(Flashback)**

After a particular violent beating from the narrow-minded villages on his fifth birthday, when they left him for dead, he appeared in some sewer. Thinking they threw him underground, he just walked around until he found a manhole to crawl out of, but after an hour of walking, he found no such sanctity, and only found himself in front of a giant cage. Asking if someone was inside, his answer was a flurry of tails grabbing him and pulling him into the cage. He was met with luscious skin on skin contact of a beautiful woman, a _naked _beautiful woman, he might add.

Her heart-shaped face, marred with tears streaking down her cheeks from her crimson eyes with slits for pupils, her black river of hair spilling down from her head with a single red streak, a pair of fluffy fox ears popping up on her head, her caramel skin, her perfect body, breasts bigger than his head, a flat, toned stomach, leading to her womanhood hid by her closed legs and plentiful hips, a firm behind with nine fox tails sprouting from her tailbone, and lets that went on for _days_.

Naruto could stare at this beauty forever, but he was concentrating on her face, her tears, specifically. "Why are you crying?" He asked softly, cupping her cheek and wiping away her tears.

The woman unconsciously leaned into the touch, his thumb brushing over her sensitive jagged whisker marks, like the one's he bore, but more feral. **"I'm sorry..." **She whispered, just loud enough for him to hear.

Naruto was confused; he just met this woman and she was sorry about something? "For? I just met you; what could you have done to me?" He asked. He froze when he finally noticed the ears and tails. "Y-you're the Kyuubi..." He whispered.

She nodded as her tears began anew and turned away from him, not wanting to see his face contort with rage at her identity. She wasn't ready when his delicate hand cupped the cheek opposite from facing him and made her look at him; she saw no malice or hatred in his eyes.

"From the way you act, it's not your fault. If you explain it to me, I'm sure I'll forgive you." He promised her. A ray of hope shining in her eyes, she nodded and sniffled, wiping her tears as she retold her tale of how the events that led to her being sealed inside him came to pass.

By the end of her story, Naruto was seething with rage at this Uchiha Madara, who attacked parents when his mother was weakened from giving birth, tore the Kyuubi out of her, which in turn killed her, and used the bijuu to attack Konoha, the Yondaime having to sacrifice his life to reseal the demon, this time in his own son.

Seeing his rage, the Kyuubi knew he despised her, and turned away, awaiting the rightful judgement.

"That fucking cock-sucker Madara!" Naruto yelled at the top of his lungs, surprising Kyuubi that a five-year old would know such language. "If I ever meet him, I'm going to cut out his eyes and force-feed him them! Then I'll saw off his arms and use them to break his legs!" As Naruto ranted about numerous ways to torture this Uchiha Madara, Kyuubi blushed that he would do such things- some of which either disturbed her or turned her on at the goriness -for _her_. She stopped Naruto mid-rant by capturing him in a hug, accidentally smothering his face in her breasts, shutting him up immediately. His face turned several shades of red not thought humanly possible, quickly warming Kyuubi's chest as she shuddered slightly and her tails wagged behind her.

**(Flashback end)**

Naruto fought the blush threatening to creep up on his face at the memory; ever since then, Kyuubi, or as he found out her real name, Hitomi, never wore clothes or hid her body, teasing him every chance she got. He was _this close _to just jumping her on more than one occasion, but the fact he was underage stayed his hand, if only barely; Kyuubi's ministrations that were in dangerous proximity to key points on his body didn't make things easier.

Where was he? Oh yes, he was about to try some of the techniques in the Forbidden Scroll of Seals! Looking through, he found a technique he thought would aid him: **Kage Bunshin. **It created solid clones, and thus needed much more chakra and less control to form them; perfect for him!

After an hour of training in the technique, he had it down. But he kept looking through the scroll, seeing if he could find anything interesting. At the bottom of the scroll he found a pair of seals, one in the shape of a double-helix, the other just a blob of darkness with a white wisp on top of it; seeing no notes around it, he put his hand to them and channeled chakra. After the poof of smoke faded, Naruto found himself staring at some translucent light blue gem, having not noticed when some inky shadow attached itself to him and sunk into his skin. Picking the gem up, he found it was as heavy as it looked, and a little cold, but exceedingly beautiful in the moonlight. He raised it to the moon to admire its beauty, but noticed in the very center, there was a red and blue glow. It was so faint; one wouldn't notice it at first. But as Naruto stared at the heart of the gem, the glow increased slowly until the gem was shining blindingly bright. With a final flash of white, it disappeared, confusing the hell out of Naruto; he didn't feel anyone take it out of his hands, he didn't drop it, it didn't just fade from his grasp, it just _disappeared _from his hands in the light!

He jumped when a familiar voice yelled behind him.

"Naruto! What do you think you're doing, stealing the Forbidden Scroll?! Do you know how much trouble you'll get in if Hokage-sama finds out?!" Umino Iruka yelled after appearing behind Naruto in a shunshin.

Spinning around faster than Iruka thought Naruto could accomplish to face him, Naruto rubbed the back of his head nervously. "Uh, hey, Iruka-sensei. What're you doing here? Did something happen to Mizuki-sensei so he sent you to pass me?" He asked, seeing if Iruka could find the underlying message about the current situation.

He was not disappointed when the Chuunin's eyes widened, then narrowed. "I see..." Iruka whispered, just in time for Mizuki to make his appearance on a branch overlooking the two of them.

"Naruto! Give me the scroll and you'll become a genin!" Mizuki said, holding his hand out for Naruto to give him the scroll, only to be met with the twin glares of the blonde and his colleague. He sneered at the demon and pulled off one of the Fuuma shuriken from his back and twirled it in his hand. "I see you got to him first, Iruka. Tell me, Naruto, do you know why the entire village hates you?" He tried a different tactic to throw them both off, but it seemed to only work on Iruka, as the scarred Chuunin yelled at him to not speak of 'it.'

Naruto only smirked slightly at the silver-haired Chuunin. "Oh, I wonder, Mizuki-teme, could it have anything to do with the Yondaime sealing the Kyuubi inside of me those twelve years ago?" He asked, smirking wildly as both Chuunin's eyes widened in shock, then Mizuki's narrowed in rage that his only ace was ineffective. Oh well, nothing a little murder could solve; he threw the large weapon at the Kyuubi brat.

Naruto ignored Iruka's yells to get out of the weapons path and snapped his hand forward, grabbing the weapon in the hole in the center, stopping it dead cold, shocking both Chuunin again, as he smirked. However, he didn't notice as his arms and hands slowly turned an ocean-green, as a light blue glow formed under his jumpsuit on his chest.

Both Chuunin eyed Naruto warily at the changes, and more so when the sclera of his eyes turned black, and his cornea and pupil turned a glowing green, every detail on his face disappearing, save for the changed eyes and his trademark whisker marks as a blue slit formed down his face, then widened into a thin diamond shape, two smaller slits sprouting from the center upwards, showing the blue glow in it, as the skin on his face turned the same green as his arms, his hair turning red and growing, two bangs forming as they lengthened well passed his chin then snapped back, two spikes of hair growing up like horns and becoming swept back as his hair seemed to shrink into his head and the skin of his head was turning red, framing the green on his face, as two strips grew out the sides of his head in the shapes of arrows, thick slots forming on them, glowing green from within, as he body continued changing. Blades grew from his shoulder blades and hips, growing out and back slightly, with more glowing green slots in them, as his arms slowly split in half, both halves turning into tendrils ending with arrow-like spikes, the right set still holding the Fuuma shuriken, as his orange jumpsuit sunk into his body, turning red in most places save for the thinning green stomach that was now more toned and had lines down it like a machine, a circle around the now-revealed blue gem in his chest, the glow of his thighs as it seemed his legs were detached from his pelvis and floated near it, and the blue slits in his upper legs. Other than those areas, he was entirely red, and looked like something completely foreign to the Elemental Nations, like a mutated virus given a body.

When Naruto was finally done transforming, both Chuunin were silent in shock at the new creature before them, only to be more shocked when they saw its shadow lift itself from the ground and formed another creature.

Black as night, tall as a fully grown man, disturbing visage, this creature was _made _of darkness. On its head was a flickering head of white hair that whipped in the air like a flame, covering its right eye, showing its narrow left eye, electric blue, as it glared at the silver-haired Chuunin before it. It had a collar of a red object, spikes lining the sides and one large spike in the front, curving up slightly, covering the lower half of the creatures face. It had a broad, powerful chest with wide shoulders, black blades of flickering obsidian flames sprouting from them, a blue orb separating them from the floating red flame-like objects, muscular arms leading to three clawed fingers on each hand. Its broad chest narrowed dangerously to the waist, two spikes on each side, as everything from the waist down was turned into a spiked black ghost-like skirt, no legs in the space below it, as two more blue orbs separated the 'hips' from another pair of red objects, a sort of 'tail' behind it made from a large black flame.

Both creatures stood before the men, their free limbs swaying in the small breeze as all was silent. On some silent signal, both figures disappeared in blurs, appearing near Mizuki, the red creature slamming its shin into the Chuunin's stomach, the black creature shoving its powerful fist into his face, rocketing him into a tree behind him, almost breaking his back. Coughing up a glob of blood and bringing his hand to his broken nose, Mizuki slowly stood back up and glared up at the red creature before him, only to gasp as the creature was changed again. It still resembled the red figure the demon became, but it was drastically different.

From head to toe, its head was now more rounded, two points sprouting from its head like a pair of animal ears, but they had green slots in them, and those damnable eyes, black seas with a glowing orb of green, staring at him unfeelingly. The red seemed to overtake the top half of its face, the green starting just under the eyes now, the blue slit halving it, the back of the creatures head growing down, like a piece of armor sculpted to resemble hair, but was stuck in the one position. The small 'wings' growing from the shoulders blades were now growing straight back from where the shoulders met the torso, the armor around those areas thickened slightly with a green band in the front, the pair of tendrils bonded into arms that grew three fingers made of orbs, a red band flowing down the arms and branching off to stop behind each orb of a fingertip. The green of its stomach grew down the pelvis to form the underbelly of the new tail it sprouted, the top half of its red like the pelvis, as the legs reconnected to the pelvis, growing a thick green band down the center of the legs as the shins snapped in half forward, creating the double knee one would see on, say, a horse, leading to two rounded green toes, a red pad on the inner parts of the feet in the air, as the glowing blue slits in the legs moved to the sides of its hips. With the way the eyes were now, molded by the brow that grew, the creature seemed to be glaring at him in fury.

Looking around for the black creature, he found it transformed into what appeared to be a similar form, of course modified for its individual characteristics. The white flame of its 'hair' was now flat against its head, still covering its left eyes, as two little wisps formed to copy the ears the red creature had, as the white flame branched off into a hose-like growth from the back of its head to between its shoulder blades, as the white continued down its back to form a large tail like its brethren had, the white continuing from under the pelvis to just under the narrow waist, the skirt-like darkness splitting in half as two legs formed like the red creature, but the two toes in front were sharpened claws, as the 'skirt' lengthened to be on level with the feet, the blue orbs and red flames at the hips disappearing, the ones at the shoulder going behind them to mimic the armor the red creature had at the shoulders, the arms narrowed but widening to the three claws, the red horn of the collar growing slightly so the point was level with its eye, as it also glared down at Mizuki with utter contempt.

The shocking part to both Chuunin was that both creatures were _floating _in the air before them. Both creatures brought their tri-fingered hands to their sides, as a black orb formed in the red creatures grasp, a glowing blue in the black creatures hands, as they formed spheres larger than their heads, as they threw them towards the Chuunin faster than he could react, exploding on impact and erasing Mizuki from existence in a splatter of blood and clang of metal breaking.

Both creatures slowly turned to face the shocked Iruka, reverting to their original forms, and the black creature sinking into the red's shadow, as the latter slowly turned back into the orange-wearing hyperactive blonde Iruka knew, who quickly fell forward, having passed out after changing back, only to be caught by Iruka, as shocked as he was.

Deciding nothing else could be done, he picked up the Forbidden Scroll and brought it, and Naruto, to the Sandaime, intent on _trying _to explain what just happened, not knowing the Hokage saw the entire ordeal through his crystal viewing ball.

**(Mindscape)**

Naruto appeared back in his mindscape, thankfully already in front of Hitomi's cage, which he turned into a meadow with small animals she could hunt as a fox, and fox kits to play with, the seal turning into a collar around Hitomi's neck, another thing she teased him with, mentioning of bondage and such.

He groaned awake, finding his head in the soft lap of Hitomi, his eyes in the perfect view of her massive breasts. Fighting down a blush and raging boner, Naruto got out of her grasp, ignoring her knowing smirk, and used his power over his mindscape to form clothes on her; why didn't he try that before?! Ignoring his own admonishment, he looked to the clothed Hitomi, smirking at her pout, and asked the question buzzing in his head. "What the fuck happened out there?" He said rather ungracefully.

**(In the Summoning Realm)**

A dark red toad with black lines across his face, horn-like growths just above his eyes, a black battle kimono with a white sash over mesh armour, and a shield on his back in the shape of a slightly cracked sake cup, as well as a sasumata, suddenly sneezed, then began complaining about how 'ungraceful' that was of him.

**(Mindscape)**

Hitomi giggled at Naruto's blunt question, but agreed; that was fucking weird, what just happened. **"Well, Naru-kun, you've released two powerful creatures from those seals you saw, and they transformed you into themselves to fight Mizuki. The red creature was known as Deoxys, the black, Darkrai. They are creatures known as 'Pokemon', creatures from another dimension that uses aura instead of chakra, yet very few individuals used it to the fullest extent. In that dimension, all altercations were solved by forcing Pokémon to fight each other, as very few humans had any fighting capabilities, rendering them useless without their Pokémon. In that dimension, there are several powerful Pokémon, two of which might be the reason why these two are here. But instead of my explaining, lets let them talk." **She explained, confusing Naruto as she gestured for him to turn around.

He did so and came face-to-face with Deoxys and Darkrai, the former staring blankly, while the latter seemed to have actual emotion, as it turned to look at Naruto. **"Hello." **it said in an ominous voice. Naruto merely waved at it. **"As the Kyuubi said, we were indeed brought here by two Pokémon, powerful ones the humans call 'Legendaries'; Dialga and Palkia. Pokémon of time and space. As such, they have the power of these titles, and are always at odds with each other, dimension/time-hopping during their fights; I was the mediator that attempts to stop them at every turn to preserve the human race, if only just barely. Deoxys is an alien virus that fell to the earth on a meteorite that mutated into its present form. In the latest fight between Dialga and Palkia, Deoxys became involved due to Palkia's spacial manipulation, and both Pokémon used their strongest attacks in an attempt to destroy each other. Striking up a truce with Deoxys, I attempted to stymie the attacks at the center, only for the collective power of four Legendaries striking at one point to create a massive spacial hemorrhage, a worm hole drawing in, for some reason, only one of every Pokémon species in existence to the center, including us. Unfortunately, that also means it wiped out all the Legendaries; anyway, within the wormhole, the DNA codes of each and every Pokémon was drawn into both me and Deoxys, and we were dropped in this time. From what I remember, we appeared after a fight between two men in red armor, one with the power to control wood, the other had red eyes and could control the Kyuubi." **Darkrai explained.

Hitomi's eyes widened. **"**_**That's **_**why you two look familiar! You appeared falling from the sky after the Shodaime fought the Uchiha ancestor, Madara! He used his damnable Sharingan to control me during the fight against Hashirama! I remember he sealed you both in what became the Forbidden Scroll, saying he could sense some great power from both of you, and in the wrong hands, it could lead to the world's destruction." **Hitomi exclaimed.

"Wait, if the Shodaime killed Madara, how'd he reappear to control you twelve years ago?" Naruto came into the conversation, pointing out the metaphorical hole in everything.

**"That was not Uchiha Madara; it was an imposter taking up his name. When we appeared, I witnessed Hashirama shove a blade through Madara's heart, and while I may not be aware of how things work for humans in this dimension, last I checked, a sword to the heart killed someone." **Darkrai corrected, showing a bit of a smartass in his comment.

"Hey, uh, how come Deoxys isn't talking?" Naruto pointed out, appearing next to the DNA pokemon, waving his hand in front of its face, only to jump when its eyes snapped to stare at him in the corner of its eyes.

**"Deoxys can't talk like I can. I am using telepathy to speak to you two in your minds, but since this **_**is **_**in your mind, I speak almost normally, save for the fact I don't have a mouth to move. Deoxys only seems to speak in his alien language, which just sounds like a bunch of shifting space." **Darkrai explained, ignoring the invisible glare from Deoxys about its 'speech impediment.'

"Oh. So, what're you guys doing in my head?" Naruto asked of them, causing everyone, excluding Deoxys, to sweatdrop at his short attention span, even if the process Darkrai was about to explain was changing him.

**"Due to you unsealing us, I immediately attached to your shadow, and Deoxys fused its heart-that gem in its chest-to you. It is our show of gratitude for saving us from the possible eternity of being inside that scroll, so we shall give you our power. We will train you to use our attacks and various forms, both fusions of other Pokémon, and in Deoxys' case, his own four forms. And just so you won't keep asking questions like 'Who's that Pokémon?', I'll be uploading every Pokémon species to your brain so you know what they are." **Darkrai explained and brought its finger to Naruto's forehead and, in a flash of light, filled it with images of every Pokémon, from Bulbasaur to Genesect, so he'd know what combinations he was made of in the future.

Naruto hissed in pain and held his head, feeling the king of all headaches, but it thankfully subsided. He glared at Darkrai for not warning him about them.

But before he could start bitching, Darkrai continued. **"And, thanks to both me and Deoxys, you will be getting what I believe you would call 'Kekkei Genkai.'" **That immediately shut Naruto up, as his twelve-year-old mind was buzzing in excitement at the idea of having Kekkei Genkai. **"Thanks to me, you'll be getting what I believe you would call Shadow Release; something those Nara's use." **Darkrai explained, drawing a confused look from Naruto on how he knows about a shinobi clan and their style of ninjutsu. **"When I gave you the information on Pokémon, I looked at your information on shinobi. But it seems you have a seal on you; several, actually, that are stunting your growth." **He explained, causing Naruto's eyes to widen. **"Ahem... the other ability you'll get is Aura Manipulation; the capability to use the energy we had in our world for numerous things. It could augment our strength, our speed, even grant us invisibility. And from Deoxys, you'll get what I think you'd call a Doujutsu. It will let you read minds of whoever you stare at, inject their minds with information you want to give them, and, due to his title as the **_**DNA **_**Pokémon, you can copy DNA sequences of people. With that, I believe you can copy other Kekkei Genkai, like those other eye things in your village. And something like that Wood manipulation that Hashi-whatever guy had." **Darkrai finished explaining.

Completely forgetting the mentioning of the multiple seals that stunted him, Naruto's eyes widened when he heard he'd be getting a Doujutsu, especially one that could let him copy of Kekkei Genkai! He could have the Sharingan, Byakugan, or any of the sub-elements in the Elemental Nations!

Wait. 'Sub-elements?' How'd he know about those?

"**I'm destroying the seals on your body, Naru-kun. And I'm not liking what I'm seeing; some of these seals allow me to look at locked-away memories that showed them actually be put on you. Naru-kun... the Sandaime ordered these to be put on you." **Hitomi explained.

End Ch. 1

Tell me what you think. So yeah, already set up for evil Sarutobi! I've wanted to try my hand at this for a while. And as we see, Naruto now holds Darkrai and Deoxys, two of my favorite Pokémon! :D And with them, the ability to transform into fused forms of every Pokémon ever (at least from Gen 1-5), which includes Deoxys' four forms, Shadow Release, Aura Release, and a Doujutsu that can copy other Kekkei Genkai. If only the only Uchiha left had the Sharingan; but _no_, he had to be a useless fuck and not get it until he almost dies. Fucking emo... Anyway, hope you like it. Also, I do not take credit for the design of Deoxys, Darkrai, and any Pokémon I will use in future chapters. That goes to **Pokemon FR **on deviantart; stuff's really awesome, guys.

Ja ne!


End file.
